first previous contents

Index

- . 3 A B C D E F G H I J K L M N O P Q R S T U V

-

  • -check
  • -maxdb
  • -maxseq
  • -no_exec_notes
  • -no_rawdata_note
  • -nocheck
  • -read_only

    • .

  • .gaprc
  • .tk_utilsrc

    • 3

  • 3 Character Amino Acids: contig editor

    • a

  • Active tags
  • Align: contig editor
  • aligned readings: printing
  • aligned readings: saving to file
  • aligned readings: sorted on alignment score
  • aligning pads: contig editor
  • Alignment matrix file
  • Alignment scores
  • allcontigs list
  • Allow del any in cons: contig editor
  • Allow del dash cons: contig editor
  • Allow del in read: contig editor
  • Allow insert any in cons: contig editor
  • Allow insert in read: contig editor
  • Allow reading shift: contig editor
  • Allow replace in cons: contig editor
  • Allow transpose any: contig editor
  • Allow uppercase: contig editor
  • allreadings list
  • Annotating contigs
  • Annotating readings
  • Annotation Selector
  • Annotation structure: doctor database
  • Annotations, searching for
  • Annotations: contig editor
  • Annotations: deleting (Doctor Database)
  • annotations: entering from a file
  • Annotations: outputting to file (Doctor Database)
  • Assemble: independently i.e. ignoring previous data
  • Assembly
  • assembly problems: breaking contigs
  • assembly problems: disassembling readings
  • assembly problems: removing readings
  • Assembly: CAP2
  • Assembly: CAP3
  • Assembly: CAP3 information
  • Assembly: directed
  • Assembly: failure codes
  • Assembly: FAKII
  • Assembly: Huang
  • Assembly: import CAP2
  • Assembly: import CAP3
  • Assembly: import FAKII
  • Assembly: into new contigs
  • Assembly: into one contig
  • Assembly: into separate contigs
  • Assembly: large projects
  • Assembly: limits
  • Assembly: maxdb
  • Assembly: maxseq
  • Assembly: Myers
  • Assembly: perform and import CAP2
  • Assembly: perform and import CAP3
  • Assembly: perform and import FAKII
  • Assembly: perform CAP2
  • Assembly: perform CAP3
  • Assembly: perform FAKII
  • Assembly: Phrap
  • Assembly: resetting limits
  • Assembly: screen only
  • Assembly: shotgun
  • Assembly: single stranded regions
  • Assembly: stack readings
  • Assembly: stand alone CAP2
  • Assembly: stand alone CAP3
  • Assembly: tips
  • Auto-display Traces: contig editor
  • Auto-save: contig editor

    • b

  • Backing up databases
  • Bap databases: conversion to gap4
  • Base accuracies - use of
  • BASE_BRIEF_FORMAT1
  • BASE_BRIEF_FORMAT2
  • Break contig
  • Break contig: contig editor
  • Busy file
  • BUSY files

    • c

  • Calculate consensus
  • Calculate consensus: algorithm
  • Calculate consensus: confidence
  • Calculate consensus: extended consensus
  • Calculate consensus: normal consensus
  • Calculate consensus: quality
  • Calculate consensus: reliability
  • Calculate consensus: unfinished consensus
  • CAP2 Assembly
  • CAP2 assembly: import
  • CAP2 assembly: perform
  • CAP2 assembly: perform and import
  • CAP2 assembly: stand alone
  • CAP3 Assembly
  • CAP3 assembly: import
  • CAP3 assembly: information
  • CAP3 assembly: perform
  • CAP3 assembly: perform and import
  • CAP3 assembly: stand alone
  • check (command line option)
  • Check assembly
  • Check database
  • Check database: annotation checks
  • Check database: clone checks
  • Check database: contig checks
  • Check database: database checks
  • Check database: ignoring
  • Check database: note checks
  • Check database: reading checks
  • Check database: template checks
  • Check database: vector checks
  • Clipping by differences
  • Clipping by quality
  • Clipping within Gap4
  • Clone structure: doctor database
  • CLOS note type
  • Colour blindness
  • Colour configuration window
  • Colour: contig editor highlight disagreements
  • Command line arguments
  • Commands menu: contig editor
  • Comparator window
  • Compare Strands: contig editor
  • Complement contig
  • Compressions: suggested experiments
  • Confidence in contig editor
  • Confidence of consensus
  • Confidence values - use of
  • Confidence values graph
  • Confidence values: editing techniques
  • Configure menus
  • configure: contig editor
  • Configure: restriction enzymes
  • Consensus algorith in contig editor
  • Consensus calculation confidence
  • Consensus calculation method
  • consensus IUB codes
  • Consensus Trace
  • Consensus: contig editor
  • Consensus: outputting
  • Consistency display
  • Contig breaking
  • Contig Comparator
  • Contig comparator: auto navigation
  • Contig Comparator: manipulating results
  • Contig comparator: next button
  • Contig complementing
  • Contig Editor: 3 Character Amino Acids
  • Contig Editor: align
  • Contig Editor: allow del any in cons
  • Contig Editor: allow del dash in cons
  • Contig Editor: Allow del in read
  • Contig Editor: allow insert any in cons
  • Contig Editor: allow insert in read
  • Contig Editor: allow reading shift
  • Contig Editor: allow replace in cons
  • Contig Editor: allow transpose any
  • Contig Editor: allow uppercase
  • Contig Editor: annotations
  • Contig Editor: auto-display traces
  • Contig Editor: auto-save
  • Contig editor: break contig
  • Contig Editor: commands menu
  • Contig Editor: Compare Strands
  • Contig editor: confidence values
  • Contig Editor: cursor
  • Contig Editor: cursor movement
  • Contig Editor: cutoff data
  • Contig Editor: cutoff values
  • Contig editor: disassemble readings
  • Contig Editor: Dump Contig
  • Contig Editor: edit by base confidence
  • Contig Editor: edit by base type
  • Contig Editor: edit mode sets
  • Contig Editor: edit modes
  • Contig Editor: editing features
  • Contig Editor: editing keys
  • Contig Editor: editing techniques
  • Contig Editor: group readings by templates
  • Contig Editor: Highlight Disagreements
  • Contig Editor: highlighting readings
  • Contig Editor: information line
  • Contig Editor: joining
  • Contig Editor: List Confidence
  • Contig Editor: mode sets
  • Contig Editor: multiple editors
  • Contig Editor: mutation reporting
  • Contig Editor: names display
  • Contig Editor: oligo selection
  • Contig Editor: primer selection
  • Contig Editor: Primer selection
  • Contig Editor: quality values
  • Contig Editor: quitting
  • Contig Editor: Reference sequence
  • Contig Editor: Reference traces
  • Contig editor: remove reading
  • Contig Editor: Save Consensus Trace
  • Contig Editor: saving
  • Contig Editor: saving configuration
  • Contig Editor: saving settings
  • Contig Editor: saving to file
  • Contig Editor: searching
  • Contig Editor: selections
  • Contig Editor: set active tags
  • Contig Editor: set default confidences
  • Contig Editor: Set or unset saving of undo
  • Contig Editor: set output list
  • Contig Editor: settings menu
  • Contig Editor: show consensus quality
  • Contig Editor: show edits
  • Contig Editor: show reading quality
  • Contig Editor: Show Strands
  • Contig Editor: shuffle Pads
  • Contig Editor: status line
  • Contig Editor: summary
  • Contig Editor: tags
  • Contig Editor: techniques
  • Contig Editor: toggle auto-save
  • Contig Editor: Trace differences
  • Contig Editor: trace display
  • Contig Editor: Trace Display menu
  • Contig Editor: translations
  • Contig Editor: translations using feature tables
  • contig joining
  • Contig names
  • contig naming
  • Contig order, reset: doctor database
  • Contig order: Contig Selector
  • Contig Selector: changing the contig order
  • Contig Selector: Contig order
  • Contig Selector: menus
  • Contig Selector: saving the contig order
  • Contig Selector: selecting contigs
  • Contig structure: doctor database
  • Contig, deletion of: doctor database
  • Contig: template display
  • CONTIG_BRIEF_FORMAT
  • contigs - identifying
  • contigs list
  • Contigs marking
  • Contigs masking
  • Contigs to Readings: lists
  • Contigs: printing
  • Contigs: saving to file
  • Convert program
  • Convert program example
  • Copy Database
  • Copy list
  • copy reads
  • Copy reads: dialogue
  • Create list
  • Creating a new database
  • Cursor: contig editor
  • Cut sites: restriction enzymes
  • Cutoff data: contig editor
  • Cutoff values: contig editor

    • d

  • Dap databases: conversion to bap or gap4
  • data hidden
  • database limits
  • Database merging
  • database readonly access
  • Database splitting
  • Database structure: doctor database
  • database write access
  • Database: backups
  • Database: busy file
  • Database: creating new
  • Database: gap4 filenames
  • database: gap4 maxdb
  • database: gap4 maxseq
  • Database: locked
  • Database: maximum size
  • Database: new
  • Database: opening
  • Database: readonly
  • Delete annotations
  • Delete contig: doctor database
  • Delete list
  • Difference clipping
  • Directed assembly
  • Directories
  • directories: trace files
  • Disassemble readings
  • Disassembly: contig editor
  • Discrepancies: searching for in contig editor
  • Doctor Database
  • Doctor database: annotation structure
  • Doctor database: clone structure
  • Doctor database: contig order
  • Doctor database: contig structure
  • Doctor database: database structure
  • Doctor database: delete contig
  • Doctor database: extending structures
  • Doctor database: note structure
  • Doctor database: original clone structure
  • Doctor database: reading structure
  • Doctor database: reset contig order
  • Doctor database: shift readings
  • Doctor database: template structure
  • Dots: contig editor highlight disagreements
  • Double strand
  • Dump Contig: contig editor

    • e

  • Edit by base confidence: contig editor
  • Edit by base type: contig editor
  • Edit list
  • Edit mode sets: contig editor
  • Edit modes: contig editor
  • Edit notebooks
  • Editing and base accuracies
  • Editing techniques
  • Editing techniques: confidence values
  • Editing techniques: overcalls
  • Editing: contig editor
  • entering annotations from file
  • Entering readings
  • entering tags from file
  • error messages: find internal joins
  • error messages: maxseq
  • Evidence for Edit1: contig editor
  • Evidence for Edit2: contig editor
  • Experiment file name length restrictions
  • Experiment file name restrictions
  • Extended consensus
  • Extending structures: doctor database
  • Extension penalty for alignments

    • f

  • FAKII Assembly
  • FAKII assembly: import
  • FAKII assembly: perform
  • FAKII assembly: perform and import
  • Fasta output from Gap
  • Feature tables: Translation in Contig Editor
  • File menu: Contig Selector
  • File name restrictions
  • File of filenames generation
  • Find internal joins
  • Find internal joins: dialogue
  • Find oligos
  • Find read pairs
  • Find read pairs: display
  • Find read pairs: example
  • Find read pairs: output
  • Find read pairs: reading lines
  • Find read pairs: template lines
  • Find repeats
  • Find sequences
  • finding joins
  • finding overlaps
  • fonts, adjusting

    • g

  • Gap penalties for alignments
  • Gap4
  • gap4 assembly limits
  • gap4 database limits: resetting
  • gap4 database sizes
  • gap4 database sizes: resetting
  • gap4 database: maxdb
  • gap4 database: maxseq
  • gap4 database: reading length limits
  • gap4 database: resetting sizes
  • gap4: resetting assembly limits
  • gap4: viewing trace files
  • gaprc
  • Genetic code
  • Green, Phil (Phrap)
  • Group Readings by Templates: contig editor
  • GTAGDB

    • h

  • Hidden data
  • hidden data
  • Hidden data: contig editor
  • Hide, in Contig Comparator
  • Highlight Disagreements: contig editor
  • Highlighting readings in the editor
  • Huang: Assembly (CAP2)
  • Huang: Assembly (CAP3)

    • i

  • identifying contigs
  • Ignore check database
  • Ignore single templates: template display
  • INFO note type
  • Information line: bases in contig editor
  • Information line: contig editor
  • Information line: contig in contig editor
  • Information line: readings in contig editor
  • Information line: tags in contig editor
  • Information, in Contig Comparator
  • Invoke contig editors, in Contig Comparator
  • Invoke contig join editors, in Contig Comparator
  • Invoke template display, in Contig Comparator
  • IUB codes: consensus

    • j

  • Join Editor
  • joining contigs

    • k

  • Keyboard summary (contig editor)

    • l

  • Labelling contigs
  • Labelling readings
  • Line thickness configuration
  • List confidence
  • List confidence: contig editor
  • Listbox
  • Lists
  • Lists: commands
  • Lists: Contigs to Readings
  • Lists: copy
  • Lists: create
  • Lists: delete
  • Lists: edit
  • Lists: load
  • Lists: minimal coverage
  • Lists: print
  • Lists: save
  • Lists: Search annotation contents
  • Lists: search sequence names
  • Lists: Search template names
  • Lists: special names
  • Lists: unattached readings
  • Load list
  • locked database
  • Long readings: suggestion of

    • m

  • marking
  • Marking contigs
  • masking
  • Masking contigs
  • Matrix for alignments
  • maxdb (command line option)
  • maxdb: gap4 assembly
  • maximum sequence length
  • maxseq
  • maxseq (command line option)
  • maxseq: find internal joins
  • maxseq: gap4 assembly
  • Menus, configuring
  • Merging databases
  • minimal coverage: lists
  • Mode sets: contig editor
  • Mutation detection: Group Readings by Templates
  • Mutation reporting: contig editor
  • Myers: Assembly (FAKII)

    • n

  • names in the editor
  • naming contigs
  • New database creation
  • Next button, in Contig comparator
  • nocheck (command line option)
  • Normal consensus
  • Note structure: doctor database
  • Notes
  • Notes: editing
  • Notes: selecting
  • Notes: special types

    • o

  • Oligo search
  • Oligo selection: contig editor
  • Oligos: choosing for probes
  • OPEN note type
  • Open penalty for alignments
  • Opening databases
  • Ordering contigs:gap4
  • Output annotations to file
  • Output enzyme by enzyme: restriction enzymes plot
  • Output ordered on position: restriction enzymes plot
  • Overcalls: editing techniques
  • overlap finding

    • p

  • pad alignment: contig editor
  • pad shuffling: contig editor
  • Phrap Assembly
  • Plot stop codons
  • Plot stop codons: examining the plot
  • Plot stop codons: updating the plot
  • Primer Selection: contig editor
  • Primer selection: contig editor
  • Primers: suggestion of
  • Print list
  • Printing contigs
  • printing: aligned readings

    • q

  • Quality calculation algorithm
  • Quality clipping
  • Quality codes
  • Quality in contig editor
  • Quality plot
  • Quality plot: examining the plot
  • Quality plot: template display
  • Quality values - use of
  • Quality values: contig editor, displayed
  • Quality values: contig editor, use within
  • Quality: output for consensus
  • Quitting: contig editor

    • r

  • RAWD note type
  • RAWDATA
  • Read pair data and contig ordering
  • Read pairs
  • read raid
  • Read-pair coverage
  • READ_BRIEF_FORMAT
  • read_only (command line option)
  • Reading coverage
  • reading length limits in gap4
  • Reading name length restrictions
  • Reading name restrictions
  • Reading names
  • reading names in the editor
  • Reading names, searching for
  • Reading numbers
  • reading percent mismatch
  • Reading plot: template display
  • Reading structure: doctor database
  • readings list
  • Readings list: template display
  • readings: copying to other databases
  • readings: entering
  • Readings: maximum in a database
  • readings: sorted on alignment score
  • readonly
  • readonly database
  • reads: copying to other databases
  • Reference sequence: contig editor
  • Reference traces: contig editor
  • Remove reading: contig editor
  • Remove, in Contig Comparator
  • Removing readings
  • Removing results
  • Repeat search
  • Report mutations: contig editor
  • Restriction enzymes
  • Restriction enzymes: configuring
  • Restriction enzymes: cut sites
  • Restriction enzymes: examining the plot
  • Restriction enzymes: selecting enzymes
  • Restriction enzymes: tags, creation of
  • Restriction enzymes: template display
  • Restriction enzymes: textual output
  • Results manager
  • Results manager: introduction
  • Results menu: Contig Selector
  • Results: removing
  • Ruler: template display

    • s

  • sample name restrictions
  • Save As
  • Save Consensus Trace: contig editor
  • Save list
  • saving contigs to file
  • Saving: contig editor
  • SCF file name restrictions
  • Screen only: assembly
  • Search annotation contents: lists
  • Search sequence names: lists
  • Search template names: lists
  • Searching by annotation comments: contig editor
  • Searching by consensus quality: contig editor
  • Searching by discrepancies: contig editor
  • Searching by edits: contig editor
  • Searching by Evidence for Edit1: contig editor
  • Searching by Evidence for Edit2: contig editor
  • Searching by file: contig editor
  • Searching by position: contig editor
  • Searching by problem: contig editor
  • Searching by quality: contig editor
  • Searching by sequence: contig editor
  • Searching by tag type: contig editor
  • Searching by Verify AND: contig editor
  • Searching reading name: contig editor
  • Searching: contig editor
  • security
  • Select tags: template display
  • selecting contigs: Contig Selector
  • Selections: contig editor
  • sequence length, maximum
  • Sequence names, searching for
  • Sequence Search
  • Set Active Tags: contig editor
  • Set Default Confidences: contig editor
  • Set genetic code
  • Set or unset saving of undo: contig editor
  • Set Output List: contig editor
  • Settings menu: contig editor
  • Settings: saving in contig editor
  • Shift readings: doctor database
  • Shotgun assembly
  • Show consensus quality: contig editor
  • Show Edits: contig editor
  • Show only read pairs: template display
  • Show reading quality: contig editor
  • Show relationships
  • Show Strands: contig editor
  • Show unpadded positions
  • Shuffle Pads: contig editor
  • simultaneous database access
  • Single stranded regions: assembling into
  • Sort Matches
  • Splitting databases
  • Status line: contig editor
  • Stop codons display
  • Stop codons: examining the plot
  • Stop codons: updating the plot
  • Stops: suggested experiments
  • strand coverage
  • string search
  • Suggest long readings
  • Suggest primers
  • Suggest probes
  • Summary of editing commands: contig editor
  • Summary: contig editor
  • Super contigs
  • Superedit: contig editor

    • t

  • Tag database
  • Tag Selector
  • TAG_BRIEF_FORMAT
  • Tags
  • Tags, searching for
  • Tags: contig editor
  • tags: entering from a file
  • Tags: restriction enzymes plot
  • Tags: template display
  • Techniques of editing
  • Template Display
  • Template display and contig ordering
  • Template display: active readings
  • Template display: contig
  • Template display: ignore single templates
  • Template display: quality plot
  • Template Display: reading plot
  • Template display: readings list
  • Template display: restriction enzymes
  • Template display: ruler
  • Template display: select tags
  • Template display: show only read pairs
  • Template display: tags
  • Template Display: template plot
  • Template names, searching for
  • Template plot: template display
  • Template structure: doctor database
  • Template: find read pairs
  • Templates: grouping readings in contig editor
  • Tips on assembly
  • tk_utilsrc
  • Toggle auto-save: contig editor
  • Trace differences: contig editor
  • Trace Display menu: contig editor
  • Trace displays: contig editor
  • Trace file location
  • trace files: defining location
  • trace files: location
  • Trace: Consensus Trace
  • Translations: contig editor

    • u

  • Unattached readings: lists
  • Undo toggle: contig editor
  • Undo: contig editor
  • Unfinished consensus
  • Unpadded base positions
  • Unpadded positions in editor
  • Update contig order
  • User levels

    • v

  • Verfiy AND: contig editor
  • Verfiy OR: contig editor
  • View menu: Contig Selector

    • first previous contents
    This page is maintained by staden-package. Last generated on 22 October 2002.
    URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_unix_177.html